R version 4.0.3 (2020-10-10) – “Bunny-Wunnies Freak Out”
Packages used for NMDS: vegan (version 2.5-7)
The document shows a series of NMDS ordinations for reference benthic communities in Virginia with environmental characteristics overlaid to evaluate natural differences in community compositions across Virginia. These NMDS will support the Genus level IBI development process. This analysis is the first run of all of reference sites in Virginia. No West Virginia DEP data is used in this analysis.Reference sites were evaluated by regional biologists.
The dataset used includes all reference stations collected in Virginia that were deemed reference through a series or water quality parameter filters and regional biologist review. If stations appeared in the dataset more than 4 times, then the most recent 4 samples were used and the rest removed. Samples that had a total number of taxa below 100 collected at the time of sampling were also removed. Taxa that occurred in the dataset <= 5% of the time were removed. The data was log10 +1 transformed. Environmental factors were compiled for each station and used to plot over the NMDS to show environmental variation associated with the community matrix. The envfit function in Vegan was used to plot the continuous environmental variables. Some environmental variables like precipitation, slope, and elevation have not been calculated for all watersheds yet and will be added at a later date.
The first step was to read in the reference site bug taxa list and environmental factors dataset for each station. Join the environmental dataset with the bug dataset to account for multiple observations of each station and collection date and time.
Check to make sure the bug and environmental join was successful:
Number of rows in Community Matrix: 684
Number or rows in Environmental Matrix: 686
The data was log10+1 transformed. Rare taxa (<=5%) were removed.
## Run 0 stress 0.1769464
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## Run 2 stress 0.1781069
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## ... Procrustes: rmse 0.003782098 max resid 0.06943787
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## ... Procrustes: rmse 0.003225147 max resid 0.05992768
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## Run 13 stress 0.1775426
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## ... New best solution
## ... Procrustes: rmse 0.003086186 max resid 0.06951657
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## ... Procrustes: rmse 0.002603155 max resid 0.06109393
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## ... Procrustes: rmse 0.003275456 max resid 0.05714009
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## ... Procrustes: rmse 0.002862363 max resid 0.06090959
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## ... Procrustes: rmse 0.003251951 max resid 0.05704288
## Run 26 stress 0.1776224
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## ... Procrustes: rmse 0.002425366 max resid 0.060838
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## ... Procrustes: rmse 0.002905321 max resid 0.04813761
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## ... Procrustes: rmse 0.003237235 max resid 0.06064025
## Run 39 stress 0.1778382
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## ... Procrustes: rmse 0.002738949 max resid 0.06971949
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## ... Procrustes: rmse 0.002622685 max resid 0.04860846
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## ... Procrustes: rmse 0.00492068 max resid 0.09048475
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## ... Procrustes: rmse 0.002193849 max resid 0.05581955
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## ... Procrustes: rmse 0.003015627 max resid 0.05593065
## Run 53 stress 0.1774996
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## ... Procrustes: rmse 0.005007727 max resid 0.08888499
## Run 56 stress 0.1779678
## Run 57 stress 0.1771667
## ... Procrustes: rmse 0.003903345 max resid 0.0697899
## Run 58 stress 0.1774129
## ... Procrustes: rmse 0.004313488 max resid 0.08610317
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## ... Procrustes: rmse 0.004597194 max resid 0.09006173
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## ... Procrustes: rmse 0.00436644 max resid 0.09158152
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## ... Procrustes: rmse 0.00387867 max resid 0.06960798
## Run 66 stress 0.1775918
## Run 67 stress 0.1769436
## ... New best solution
## ... Procrustes: rmse 0.003434656 max resid 0.06916175
## Run 68 stress 0.1776042
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## ... Procrustes: rmse 0.00346652 max resid 0.04930093
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## ... Procrustes: rmse 0.002588364 max resid 0.04874967
## Run 79 stress 0.1782058
## Run 80 stress 0.1771403
## ... Procrustes: rmse 0.003541084 max resid 0.06921202
## Run 81 stress 0.1769346
## ... New best solution
## ... Procrustes: rmse 0.003649282 max resid 0.06888104
## Run 82 stress 0.1772535
## ... Procrustes: rmse 0.005006741 max resid 0.08889739
## Run 83 stress 0.177702
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## ... Procrustes: rmse 0.004763335 max resid 0.09073254
## Run 85 stress 0.1769141
## ... New best solution
## ... Procrustes: rmse 0.002297921 max resid 0.04674016
## Run 86 stress 0.1778882
## Run 87 stress 0.1780537
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## ... Procrustes: rmse 0.003027078 max resid 0.06113366
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## ... Procrustes: rmse 0.003759436 max resid 0.06997966
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## ... Procrustes: rmse 0.004021796 max resid 0.06919823
## Run 102 stress 0.1778451
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## ... Procrustes: rmse 0.004624966 max resid 0.08984473
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## ... Procrustes: rmse 0.003825104 max resid 0.06896805
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## ... Procrustes: rmse 0.002514178 max resid 0.0485171
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## ... Procrustes: rmse 0.003803221 max resid 0.0889332
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## ... Procrustes: rmse 0.002801216 max resid 0.05579458
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## Run 122 stress 0.1778096
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## ... Procrustes: rmse 0.001531566 max resid 0.03292553
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## ... Procrustes: rmse 0.004285716 max resid 0.0692711
## Run 131 stress 0.1776481
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## Run 134 stress 0.1773478
## ... Procrustes: rmse 0.004307295 max resid 0.06931037
## Run 135 stress 0.1771425
## ... Procrustes: rmse 0.002265401 max resid 0.04850048
## Run 136 stress 0.1769131
## ... New best solution
## ... Procrustes: rmse 0.001018166 max resid 0.02214304
## Run 137 stress 0.1782359
## Run 138 stress 0.1830455
## Run 139 stress 0.1778075
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## ... Procrustes: rmse 0.00268917 max resid 0.06071233
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## ... Procrustes: rmse 0.004259239 max resid 0.090938
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## ... Procrustes: rmse 0.00467722 max resid 0.09085539
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## ... Procrustes: rmse 0.003314654 max resid 0.05554797
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## ... Procrustes: rmse 0.003427061 max resid 0.05560988
## Run 153 stress 0.1782
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## ... Procrustes: rmse 0.002757385 max resid 0.06053595
## Run 159 stress 0.1774947
## Run 160 stress 0.1776804
## Run 161 stress 0.1781307
## Run 162 stress 0.1774941
## Run 163 stress 0.1771227
## ... Procrustes: rmse 0.004347746 max resid 0.06907252
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## ... Procrustes: rmse 0.002708655 max resid 0.06928976
## Run 165 stress 0.1771415
## ... Procrustes: rmse 0.002308852 max resid 0.04839257
## Run 166 stress 0.1774944
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## ... Procrustes: rmse 0.004376215 max resid 0.09089875
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## ... Procrustes: rmse 0.004335 max resid 0.07028166
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## ... Procrustes: rmse 0.002693509 max resid 0.06956839
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## ... Procrustes: rmse 0.004987594 max resid 0.08612174
## Run 180 stress 0.1780175
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## Run 190 stress 0.1771443
## ... Procrustes: rmse 0.001991563 max resid 0.04848497
## Run 191 stress 0.1771511
## ... Procrustes: rmse 0.003686216 max resid 0.06979451
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## ... Procrustes: rmse 0.003401501 max resid 0.05706404
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## Run 197 stress 0.1778236
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## ... Procrustes: rmse 0.003711046 max resid 0.09169506
## Run 200 stress 0.1776086
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## ... Procrustes: rmse 0.00412917 max resid 0.06872876
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## Run 208 stress 0.17734
## ... Procrustes: rmse 0.00376764 max resid 0.05554373
## Run 209 stress 0.1777039
## Run 210 stress 0.1775306
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## Run 212 stress 0.1777198
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## Run 214 stress 0.1773448
## ... Procrustes: rmse 0.005422783 max resid 0.09162234
## Run 215 stress 0.1776661
## Run 216 stress 0.1771369
## ... Procrustes: rmse 0.004173637 max resid 0.06926683
## Run 217 stress 0.1773297
## ... Procrustes: rmse 0.003594641 max resid 0.06984964
## Run 218 stress 0.1772392
## ... Procrustes: rmse 0.004061257 max resid 0.09002815
## Run 219 stress 0.1777646
## Run 220 stress 0.1771759
## ... Procrustes: rmse 0.002838411 max resid 0.04789021
## Run 221 stress 0.1771567
## ... Procrustes: rmse 0.004334244 max resid 0.06813162
## Run 222 stress 0.1777114
## Run 223 stress 0.1785162
## Run 224 stress 0.1775866
## Run 225 stress 0.1773523
## ... Procrustes: rmse 0.004170587 max resid 0.0692641
## Run 226 stress 0.1773182
## ... Procrustes: rmse 0.003984145 max resid 0.07013213
## Run 227 stress 0.177206
## ... Procrustes: rmse 0.003788673 max resid 0.08864991
## Run 228 stress 0.1782295
## Run 229 stress 0.1773515
## ... Procrustes: rmse 0.004164924 max resid 0.07017405
## Run 230 stress 0.1775961
## Run 231 stress 0.1785413
## Run 232 stress 0.1797321
## Run 233 stress 0.1781377
## Run 234 stress 0.1839927
## Run 235 stress 0.1769431
## ... Procrustes: rmse 0.002719893 max resid 0.0697436
## Run 236 stress 0.1774071
## ... Procrustes: rmse 0.003998681 max resid 0.06915102
## Run 237 stress 0.1772094
## ... Procrustes: rmse 0.003923345 max resid 0.09175396
## Run 238 stress 0.1838455
## Run 239 stress 0.1779333
## Run 240 stress 0.1774057
## ... Procrustes: rmse 0.004010652 max resid 0.06949246
## Run 241 stress 0.1769367
## ... Procrustes: rmse 0.002624068 max resid 0.04858377
## Run 242 stress 0.1790692
## Run 243 stress 0.1779699
## Run 244 stress 0.1777464
## Run 245 stress 0.1772669
## ... Procrustes: rmse 0.005058909 max resid 0.09152404
## Run 246 stress 0.1769331
## ... Procrustes: rmse 0.003206283 max resid 0.06967267
## Run 247 stress 0.1787574
## Run 248 stress 0.1785889
## Run 249 stress 0.1769118
## ... New best solution
## ... Procrustes: rmse 0.0004503772 max resid 0.00943879
## ... Similar to previous best
## *** Solution reached
##
## Call:
## metaMDS(comm = NoncoastalFive[, 6:106], k = 3, trymax = 1000)
##
## global Multidimensional Scaling using monoMDS
##
## Data: NoncoastalFive[, 6:106]
## Distance: bray
##
## Dimensions: 3
## Stress: 0.1769118
## Stress type 1, weak ties
## Two convergent solutions found after 249 tries
## Scaling: centring, PC rotation, halfchange scaling
## Species: expanded scores based on 'NoncoastalFive[, 6:106]'
## NMDS1 NMDS2 r2 Pr(>r)
## Year 0.99879 0.04917 0.0325 0.07 .
## JulianDate -0.40242 0.91546 0.6995 0.01 **
## Latitude -0.75648 -0.65402 0.0011 0.84
## Longitude -0.40393 -0.91479 0.0022 0.75
## totalArea_sqMile -0.74576 -0.66621 0.3672 0.01 **
## ELEVMEAN 0.93606 0.35184 0.1899 0.01 **
## SLPMEAN 0.92034 0.39113 0.1192 0.01 **
## wshdRain_mmyr -0.73380 -0.67936 0.3517 0.01 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Permutation: free
## Number of permutations: 99
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$Season, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Fall Spring
## delta 0.6252 0.6188
## n 346 338
##
## Chance corrected within-group agreement A: 0.04881
## Based on observed delta 0.622 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$US_L3NAME, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Blue Ridge Central Appalachians Northern Piedmont Piedmont
## delta 0.5942 0.6021 0.641 0.6099
## n 154 40 101 137
## Ridge and Valley
## delta 0.657
## n 252
##
## Chance corrected within-group agreement A: 0.03989
## Based on observed delta 0.6278 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$Basin_Code, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Appomattox Chowan-Dismal James-Middle James-Upper New Potomac-Lower
## delta 0.5234 0.533 0.6089 0.6534 0.65 0.6371
## n 12 4 61 114 78 25
## Potomac-Shenandoah Rappahannock Roanoke Tennessee-Big Sandy
## delta 0.6547 0.6355 0.6094 0.5991
## n 41 122 87 16
## Tennessee-Clinch Tennessee-Holston Yadkin York
## delta 0.6243 0.6247 0.5727 0.5843
## n 50 53 4 17
##
## Chance corrected within-group agreement A: 0.03817
## Based on observed delta 0.629 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$ASSESS_REG, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## BRRO NRO PRO SWRO VRO
## delta 0.642 0.6509 0.5783 0.6316 0.6428
## n 244 158 17 156 109
##
## Chance corrected within-group agreement A: 0.02092
## Based on observed delta 0.6402 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##Bioregion: Non-Coastal
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$Bioregion, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Mountain Piedmont
## delta 0.6467 0.6334
## n 446 238
##
## Chance corrected within-group agreement A: 0.01815
## Based on observed delta 0.642 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
#Bioregion separated by Season
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$Gradient, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MACS Riffle
## delta 0.5603 0.653
## n 9 675
##
## Chance corrected within-group agreement A: 0.003271
## Based on observed delta 0.6518 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$Order, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## 1 2 3 4 5
## delta 0.6253 0.6542 0.6189 0.5751 0.5404
## n 243 205 137 74 25
##
## Chance corrected within-group agreement A: 0.04556
## Based on observed delta 0.6241 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$StreamCate, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Large Medium Small
## delta 0.5683 0.6189 0.6463
## n 99 137 448
##
## Chance corrected within-group agreement A: 0.03734
## Based on observed delta 0.6295 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$WQS_CLASS, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## III IV V VI
## delta 0.6369 0.6438 0.6304 0.6007
## n 210 184 87 203
##
## Chance corrected within-group agreement A: 0.04084
## Based on observed delta 0.6272 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$WQS_TROUT, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## Yes
## delta 0.6496 0.6215
## n 394 290
##
## Chance corrected within-group agreement A: 0.02479
## Based on observed delta 0.6377 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$BioregionSeason, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## MountainFall MountainSpring PiedmontFall PiedmontSpring
## delta 0.6224 0.6048 0.5882 0.6099
## n 225 221 121 117
##
## Chance corrected within-group agreement A: 0.06941
## Based on observed delta 0.6085 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999
##
## Call:
## mrpp(dat = bugsnms_noncoast[, 6:106], grouping = samplescoresenv_noncoast$Bioregionsize, distance = "bray")
##
## Dissimilarity index: bray
## Weights for groups: n
##
## Class means and counts:
##
## LargeMountainFall LargeMountainSpring LargePiedmontFall
## delta 0.4813 0.5485 0.5099
## n 29 27 22
## LargePiedmontSpring MediumMountainFall MediumMountainSpring
## delta 0.5404 0.5719 0.5646
## n 21 51 50
## MediumPiedmontFall MediumPiedmontSpring SmallMountainFall
## delta 0.5618 0.6105 0.6095
## n 18 18 145
## SmallMountainSpring SmallPiedmontFall SmallPiedmontSpring
## delta 0.5764 0.5808 0.591
## n 144 81 78
##
## Chance corrected within-group agreement A: 0.1183
## Based on observed delta 0.5765 and expected delta 0.6539
##
## Significance of delta: 0.001
## Permutation: free
## Number of permutations: 999